Rapid detection and typing of influenza virus and identification of its various strains is critical to identification and control of a potential human pandemic. Influenza virus is composed of eight single-stranded RNA molecules (HA, NA, PB2, PB1, PA, NS, M, NP) that code for eleven specific proteins. The RNA for the matrix protein (M) is relatively conserved and is therefore used to detect and distinguish a Type A virus. M can also be used to detect and distinguish H5N1.
The hemagglutinin protein (HA) and neuraminidase protein (NA) are grouped into 16 and 9 subtypes, respectively, both have high sequence variability even within subtypes and thus provide an effective means of monitoring changes that might occur in a virus. The HA protein protrudes from the surface of the virus and allows it to attach to a cell to begin the infection cascade. The NA protein is also located on the surface of the virus and allows the release of new particles within the infected cell.
Currently the Eurasian H5N1 virus infects only the lower lungs in human and is therefore less readily transmitted human-to-human than annual strains of human influenza that infect the upper respiratory track. But, mutations within the HA and NA RNAs are frequent and alter viral infectivity and lethality in different hosts and their tissues. In addition, gene assortment among the different viral subtypes is another very worrisome feature of influenza and could result in recombining RNA sequences for high infectivity in humans with high lethality.